Updated project metadata. Prostate cancer (PCa) is the most common malignant tumour, with high incidence rates and heterogeneity in men around the world. It is becoming an increasing burden on the health care system due to lack of tests for precise detection of disease, risk assessment and response to treatments. We used SWATH-MS as a discovery proteomics tool to identify markers in the serum of newly diagnosed PCa patients and healthy controls to facilitate the improved diagnosis. Furthermore, identification and expression of proteins was also determined in patients undergone radiotherapy and prostatectomy for monitoring of the clinical response to respective treatment options. Thus, this study provides the basis for a proteomic signature to improve diagnostics of patients with localised prostate cancer.